Biology subjects

Porth, I.

Publications and source records attributed to Porth, I..

7 recordsLinked to original sources

bioRxiv2026

Male-biased triploidy in Populus tremuloides and genomic structure of its southern relict populations

PremiseIsolated populations at the southern range edge of aspen (Populus tremuloides Michx.) offer a unique opportunity to study ploidy, clonality and distribution of sex under arid, high-elevation conditions. We aimed to characterize such traits, including potential sex biases and associations with ploidy, investigating previously unexamined Texan populations in a range-wide genomic framework of genetic structure and demographic history of this keystone species. MethodsWe combined new genotypic data from western Texas (Davis Mountains, Big Bend, Guadalupe Mountains) with preexisting datasets, assessing range-wide genetic diversity, clonality, ploidy, and sex. We further conducted ADMIXTURE and phylogenetic analyses, reconstructed historical effective population sizes (Ne) with Stairway Plot 2. ResultsTexan stands revealed high clonality, with diploid and triploid genets. Most Davis and Guadalupe Mountain individuals clustered with a southwestern U.S. lineage of aspen, whereas Big Bend individuals grouped with a Mexican, demonstrating for the first time the continuous northward geographic distributions of allele frequencies in aspen coherent with phylogenetics. The significant male bias in sex ratios, particularly among triploids, suggests dimorphism in survival or reproduction. No effect of elevation on sex was identified. Demographic inference indicated an ancient bottleneck ([~]1-2 Mya) common to all six lineages, but more recent historical Ne trajectories differ between the northern and southern regions. ConclusionsThese findings shed light on how clonality, ploidy, and sex have interacted in shaping dioecious plant species, highlighting the importance of incorporating such information into projections of how climate change and habitat loss will affect their distribution, abundance, and the extinction risk of their marginal populations.

evolutionary biology↗

bioRxiv2025

Elucidating continental-wide phylogeographic and adaptive processes shaping the genome-wide diversity of North America's most widely distributed tree

Past population dynamics during the Pleistocene ice age and the Holocene era have profoundly influenced the genetic structure and diversity of species. Environmental heterogeneity has further shaped local and regional adaptive variation. Here, we ask how historical processes have led to the current genetic diversity of a key North American species across its vast natural range and what genomic signatures indicate regional adaptive divergence and local adaptation. We used sequencing data from 1,903 Populus tremuloides Michx. (quaking aspen) trees to assess historical population dynamics and identify genotype-environment associations within and among the species major genetic lineages. The two northern and western North American aspen lineages exhibited historical population expansion patterns, while the southernmost lineage experienced a historical bottleneck consistent with past glacial oscillations. We found that the earliest split between genetic lineages of P. tremuloides occurred in the southern part of its distribution range. We further identified larger blocks of adaptive SNPs within separate genomic sequence regions on chromosomes 2 and 8 that may exhibit suppressed genetic recombination, contributing to the maintenance of regional and local adaptation in the species. Our study provides key insights into the evolutionary processes affecting adaptive genetic variation and phylogeography at a broad continental and regional scale, with implications for predicting species responses to future climate change.

evolutionary biology↗

bioRxiv2025

Soil microbiomes reveal different strategies for nitrogen acquisition in aspen-dominated stands from Mexico and Canada

Plant species shape soil microbiome composition through species-specific interactions. However, it is less clear how these interactions vary across populations that diverged a long time ago. In this study, we explore the influence of host genetic composition and edaphic factors on the soil microbiome of Populus tremuloides, one of North Americas most widespread tree species. Using 16S, 18S rRNA gene, and ITS2 region metabarcoding on soils from natural stands and potting mix, rhizosphere, and root samples from a greenhouse common garden, we examined prokaryotic and fungal communities in two aspen genetic groups. The Eastern Canada group represents boreal and cold temperate ecoregions, and the one from Northwestern Mexico represents warm temperate ecoregion. Variation in microbial community structure correlated with soil properties but results from common gardens indicated that the host genetic makeup may also play a role. The three ecoregions showed functional divergence: warm temperate sites hosted a higher abundance and diversity of nitrogen-fixing bacteria, while boreal stands exhibited stronger associations with ectomycorrhizal fungi. Our findings highlight how local adaptations to climate and soil conditions in aspen extend to their microbial partners, emphasizing the potential role of host-microbe interactions in shaping tree resilience and susceptibility to future climate changes.

evolutionary biology↗

bioRxiv2023

Structural genomic variations and their effects on phenotypes in Populus

DNA copy numbers have recently emerged as an important new marker system. In the absence of a contiguous reference genome, alternative detection systems such as the comparative hybridization method have been used to detect copy number variations (CNVs). With the advent of chromosome-level resolved reference genomes based on the incorporation of long-read sequencing and powerful bioinformatics pipelines, comprehensive detection of all structural variations (SVs) in the poplar genome is now within reach. Gene CNVs and their inheritance are important because they can cause dosage effects in phenotypic variations. These are potent genetic markers that should be considered in complex trait variation such as growth and adaptation in poplar. SVs such as CNVs could be used in future genomic selection studies for poplar, especially in cases when heterosis increases hybrid performance (hybrid vigor). This Chapter reports recent findings on SVs in natural populations of Populus spp. as well as on artificially induced SVs in poplar to understand their potential importance in generating a considerable amount of phenotypic improvement. The Chapter concludes with an outlook on the future implementation of knowledge on SVs in poplar crop breeding.

plant biology↗

bioRxiv2022

Multi-trait selection to build resilience in conifer forests: a case study on spruce-shoot weevil interactions

Tree planting programs now need to consider climate change increasingly, therefore, the resistance to pests plays an essential role in enabling tree adaptation to new ranges through tree population movement. The weevil Pissodes strobi (Peck) is a major pest of spruces and substantially reduces lumber quality. We revisited a large Interior spruce provenance/progeny trial (2,964 genotypes, 42 families) of varying susceptibility, established in British Columbia. We employed multivariate mixed linear models to estimate covariances between, and genetic control of, juvenile height growth and resistance traits. We performed linear regressions and ordinal logistic regressions to test for impact of parental origin on growth and susceptibility to the pest, respectively. A significant environmental component affected the correlations between resistance and height, with outcomes dependent on families. Parents sourced from above 950 m a.s.l. elevation negatively influenced host resistance to attacks, probably due to higher P. engelmannii proportion. For the genetic contribution of parents sourced from above 1,200 m a.s.l., however, we found less attack severity, probably due to a marked mismatch in phenologies. This clearly highlights that hybrid status might be a good predictor for weevil attacks and delineates the boundaries of successful spruce population movement. Families resulting from crossing susceptible with resistant parents generally showed fast-growing trees were the least affected by weevil attacks. Such results indicate that these "hybrids" might be genetically better equipped with an optimized resource allocation between defence and growth and might provide the solution for concurrent improvement in resistance against weevil attacks, whilst maintaining tree productivity.

genetics↗

bioRxiv2019

Inter- and Intra-Generation Genomic Predictions for Douglas-fir Growth in Unobserved Environments

Conifers are prime candidates for genomic selection (GS) due to their long breeding cycles. Previous studies have shown much reduced prediction accuracies (PA) of breeding values in unobserved environments, which may impede its adoption. The impact of explicit environmental heterogeneity modeling including genotype-by-environment (GxE) interaction effects using environmental covariates (EC) in a reaction-norm genomic prediction model was tested using single-step GBLUP (ssGBLUP). A three-generation coastal Douglas-fir experimental population with 14 genetic trials (n = 13,615) permitted estimation of intra- and inter-generation PA in unobserved environments using 66,969 SNPs derived from exome capture. Intra- and inter-generation PAs ranged from 0.447-0.640 and 0.317-0.538, respectively. The inclusion of ECs in the prediction models explained up to 23% of the phenotypic variation for the fully specified model and resulted in the best model fit. Modeling GxE effects in the training population increased PA up to 6% and 13% over the base model for inter- and intra-generations, respectively. GS-PA can be substantially improved using ECs to explain environmental heterogeneity and GxE effects. The ssGBLUP methodology allows historical genetic trials containing non-genotyped samples to contribute in genomic prediction, and, thus, effectively boosting training population size which is a critical step. Further pheno- and enviro-typing developments may improve GS-PA.

genetics↗

bioRxiv2018

Partial correlation analysis of transcriptomes helps detangle the growth and defense network in spruce

O_LIIn plants, there can be a trade-off between resource allocations to growth versus defense. Here, we use partial correlation analysis of gene expression to make inferences about the nature of this interaction.\nC_LIO_LIWe studied segregating progenies of Interior spruce subject to weevil attack. In a controlled experiment, we measured pre-attack plant growth and post-attack damage with several morphological measures, and profiled transcriptomes of 188 progeny.\nC_LIO_LIWe used partial correlations of individual transcripts (ESTs) with pairs of growth/defense traits to identify important nodes and edges in the inferred underlying gene network, e.g., those pairs of growth/defense traits with high mutual correlation with a single EST transcript. We give a method to identify such ESTs.\nC_LIO_LIA terpenoid ABC transporter gene showed strongest correlations (P=0.019); its transcript represented a hub within the compact 166-member gene-gene interaction network (P=0.004) of the negative genetic correlations between growth and subsequent pest attack. A small 21-member interaction network (P=0.004) represented the uncovered positive correlations.\nC_LIO_LIOur study demonstrates partial correlation analysis identifies important gene networks underlying growth and susceptibility to the weevil in spruce. In particular, we found transcripts that strongly modify the trade-off between growth and defense, and allow identification of networks more central to the trade-off.\nC_LI

plant biology↗